This dashboard helps facilitate the CQI analyses VIHA E.C.R. (early cognitive recline) project.
By implementing plans for self-care activities with established clients, primary caregivers will see a mean score reduction of at least 4 points on the ECR after 4 months of self-care activities by Dec 1, 2018.
Report rendered by wibeasley at 2020-02-12, 22:56 -0600 in 9 seconds.
For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand. But you’ll probably regret it.
| name | value |
|---|---|
| version | R version 3.6.2 (2019-12-12) |
| os | Ubuntu 19.10 |
| system | x86_64, linux-gnu |
| ui | X11 |
| language | (EN) |
| collate | en_US.UTF-8 |
| ctype | en_US.UTF-8 |
| tz | America/Chicago |
| date | 2020-02-12 |
| package | ondiskversion | loadedversion | attached | is_base | date | source |
|---|---|---|---|---|---|---|
| assertthat | 0.2.1 | 0.2.1 | FALSE | FALSE | 2019-03-21 | CRAN (R 3.6.1) |
| backports | 1.1.5 | 1.1.5 | FALSE | FALSE | 2019-10-02 | CRAN (R 3.6.1) |
| broom | 0.5.4 | 0.5.4 | FALSE | FALSE | 2020-01-27 | CRAN (R 3.6.2) |
| Cairo | 1.5.10 | 1.5-10 | FALSE | FALSE | 2019-03-28 | CRAN (R 3.6.1) |
| callr | 3.4.1 | 3.4.1 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| cli | 2.0.1 | 2.0.1 | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.1) |
| colorspace | 1.4.1 | 1.4-1 | FALSE | FALSE | 2019-03-18 | CRAN (R 3.6.1) |
| config | 0.3 | 0.3 | FALSE | FALSE | 2018-03-27 | CRAN (R 3.6.1) |
| crayon | 1.3.4 | 1.3.4 | FALSE | FALSE | 2017-09-16 | CRAN (R 3.6.1) |
| crosstalk | 1.0.0 | 1.0.0 | FALSE | FALSE | 2016-12-21 | CRAN (R 3.6.1) |
| data.table | 1.12.8 | 1.12.8 | FALSE | FALSE | 2019-12-09 | CRAN (R 3.6.1) |
| desc | 1.2.0 | 1.2.0 | FALSE | FALSE | 2018-05-01 | CRAN (R 3.6.1) |
| devtools | 2.2.1 | 2.2.1 | FALSE | FALSE | 2019-09-24 | CRAN (R 3.6.1) |
| digest | 0.6.23 | 0.6.23 | FALSE | FALSE | 2019-11-23 | CRAN (R 3.6.1) |
| dplyr | 0.8.4 | 0.8.4 | FALSE | FALSE | 2020-01-31 | CRAN (R 3.6.2) |
| DT | 0.12 | 0.12 | FALSE | FALSE | 2020-02-05 | CRAN (R 3.6.2) |
| ellipsis | 0.3.0 | 0.3.0 | FALSE | FALSE | 2019-09-20 | CRAN (R 3.6.1) |
| evaluate | 0.14 | 0.14 | FALSE | FALSE | 2019-05-28 | CRAN (R 3.6.1) |
| fansi | 0.4.1 | 0.4.1 | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.1) |
| farver | 2.0.3 | 2.0.3 | FALSE | FALSE | 2020-01-16 | CRAN (R 3.6.1) |
| fastmap | 1.0.1 | 1.0.1 | FALSE | FALSE | 2019-10-08 | CRAN (R 3.6.1) |
| flexdashboard | 0.5.1.1 | 0.5.1.1 | TRUE | FALSE | 2018-06-29 | CRAN (R 3.6.1) |
| fs | 1.3.1 | 1.3.1 | FALSE | FALSE | 2019-05-06 | CRAN (R 3.6.1) |
| generics | 0.0.2 | 0.0.2 | FALSE | FALSE | 2018-11-29 | CRAN (R 3.6.1) |
| ggplot2 | 3.2.1 | 3.2.1 | TRUE | FALSE | 2019-08-10 | CRAN (R 3.6.1) |
| glue | 1.3.1 | 1.3.1 | FALSE | FALSE | 2019-03-12 | CRAN (R 3.6.1) |
| gtable | 0.3.0 | 0.3.0 | FALSE | FALSE | 2019-03-25 | CRAN (R 3.6.1) |
| highr | 0.8 | 0.8 | FALSE | FALSE | 2019-03-20 | CRAN (R 3.6.1) |
| hms | 0.5.3 | 0.5.3 | FALSE | FALSE | 2020-01-08 | CRAN (R 3.6.1) |
| htmltools | 0.4.0 | 0.4.0 | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.1) |
| htmlwidgets | 1.5.1 | 1.5.1 | FALSE | FALSE | 2019-10-08 | CRAN (R 3.6.1) |
| httpuv | 1.5.2 | 1.5.2 | FALSE | FALSE | 2019-09-11 | CRAN (R 3.6.1) |
| httr | 1.4.1 | 1.4.1 | FALSE | FALSE | 2019-08-05 | CRAN (R 3.6.1) |
| import | 1.1.0 | 1.1.0 | FALSE | FALSE | 2015-06-22 | CRAN (R 3.6.1) |
| jsonlite | 1.6.1 | 1.6.1 | FALSE | FALSE | 2020-02-02 | CRAN (R 3.6.2) |
| kableExtra | 1.1.0 | 1.1.0 | FALSE | FALSE | 2019-03-16 | CRAN (R 3.6.1) |
| knitr | 1.28 | 1.28 | TRUE | FALSE | 2020-02-06 | CRAN (R 3.6.2) |
| labeling | 0.3 | 0.3 | FALSE | FALSE | 2014-08-23 | CRAN (R 3.6.1) |
| later | 1.0.0 | 1.0.0 | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.1) |
| lattice | 0.20.38 | 0.20-38 | FALSE | FALSE | 2018-11-04 | CRAN (R 3.6.1) |
| lazyeval | 0.2.2 | 0.2.2 | FALSE | FALSE | 2019-03-15 | CRAN (R 3.6.1) |
| lifecycle | 0.1.0 | 0.1.0 | FALSE | FALSE | 2019-08-01 | CRAN (R 3.6.1) |
| magrittr | 1.5 | 1.5 | FALSE | FALSE | 2014-11-22 | CRAN (R 3.6.1) |
| memoise | 1.1.0 | 1.1.0 | FALSE | FALSE | 2017-04-21 | CRAN (R 3.6.1) |
| mime | 0.9 | 0.9 | FALSE | FALSE | 2020-02-04 | CRAN (R 3.6.2) |
| munsell | 0.5.0 | 0.5.0 | FALSE | FALSE | 2018-06-12 | CRAN (R 3.6.1) |
| nlme | 3.1.144 | 3.1-144 | FALSE | FALSE | 2020-02-06 | CRAN (R 3.6.2) |
| pillar | 1.4.3 | 1.4.3 | FALSE | FALSE | 2019-12-20 | CRAN (R 3.6.1) |
| pkgbuild | 1.0.6 | 1.0.6 | FALSE | FALSE | 2019-10-09 | CRAN (R 3.6.1) |
| pkgconfig | 2.0.3 | 2.0.3 | FALSE | FALSE | 2019-09-22 | CRAN (R 3.6.1) |
| pkgload | 1.0.2 | 1.0.2 | FALSE | FALSE | 2018-10-29 | CRAN (R 3.6.1) |
| plotly | 4.9.1 | 4.9.1 | TRUE | FALSE | 2019-11-07 | CRAN (R 3.6.1) |
| prettyunits | 1.1.1 | 1.1.1 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| processx | 3.4.2 | 3.4.2 | FALSE | FALSE | 2020-02-09 | CRAN (R 3.6.2) |
| promises | 1.1.0 | 1.1.0 | FALSE | FALSE | 2019-10-04 | CRAN (R 3.6.1) |
| ps | 1.3.0 | 1.3.0 | FALSE | FALSE | 2018-12-21 | CRAN (R 3.6.1) |
| purrr | 0.3.3 | 0.3.3 | FALSE | FALSE | 2019-10-18 | CRAN (R 3.6.1) |
| R6 | 2.4.1 | 2.4.1 | FALSE | FALSE | 2019-11-12 | CRAN (R 3.6.1) |
| RColorBrewer | 1.1.2 | 1.1-2 | FALSE | FALSE | 2014-12-07 | CRAN (R 3.6.1) |
| Rcpp | 1.0.3 | 1.0.3 | FALSE | FALSE | 2019-11-08 | CRAN (R 3.6.1) |
| readr | 1.3.1 | 1.3.1 | FALSE | FALSE | 2018-12-21 | CRAN (R 3.6.1) |
| remotes | 2.1.0 | 2.1.0 | FALSE | FALSE | 2019-06-24 | CRAN (R 3.6.1) |
| rlang | 0.4.4 | 0.4.4 | FALSE | FALSE | 2020-01-28 | CRAN (R 3.6.2) |
| rmarkdown | 2.1 | 2.1 | FALSE | FALSE | 2020-01-20 | CRAN (R 3.6.2) |
| rprojroot | 1.3.2 | 1.3-2 | FALSE | FALSE | 2018-01-03 | CRAN (R 3.6.1) |
| rstudioapi | 0.11 | 0.11 | FALSE | FALSE | 2020-02-07 | CRAN (R 3.6.2) |
| rvest | 0.3.5 | 0.3.5 | FALSE | FALSE | 2019-11-08 | CRAN (R 3.6.1) |
| scales | 1.1.0 | 1.1.0 | FALSE | FALSE | 2019-11-18 | CRAN (R 3.6.1) |
| sessioninfo | 1.1.1 | 1.1.1 | FALSE | FALSE | 2018-11-05 | CRAN (R 3.6.1) |
| shiny | 1.4.0 | 1.4.0 | FALSE | FALSE | 2019-10-10 | CRAN (R 3.6.1) |
| stringi | 1.4.5 | 1.4.5 | FALSE | FALSE | 2020-01-11 | CRAN (R 3.6.1) |
| stringr | 1.4.0 | 1.4.0 | FALSE | FALSE | 2019-02-10 | CRAN (R 3.6.1) |
| TabularManifest | 0.1.16.9003 | 0.1-16.9003 | FALSE | FALSE | 2019-11-16 | Github (Melinae/TabularManifest@4cbc21c) |
| testthat | 2.3.1 | 2.3.1 | FALSE | FALSE | 2019-12-01 | CRAN (R 3.6.1) |
| tibble | 2.1.3 | 2.1.3 | FALSE | FALSE | 2019-06-06 | CRAN (R 3.6.1) |
| tidyr | 1.0.2 | 1.0.2 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| tidyselect | 1.0.0 | 1.0.0 | FALSE | FALSE | 2020-01-27 | CRAN (R 3.6.2) |
| usethis | 1.5.1 | 1.5.1 | FALSE | FALSE | 2019-07-04 | CRAN (R 3.6.1) |
| vctrs | 0.2.2 | 0.2.2 | FALSE | FALSE | 2020-01-24 | CRAN (R 3.6.2) |
| viridisLite | 0.3.0 | 0.3.0 | FALSE | FALSE | 2018-02-01 | CRAN (R 3.6.1) |
| webshot | 0.5.2 | 0.5.2 | FALSE | FALSE | 2019-11-22 | CRAN (R 3.6.1) |
| withr | 2.1.2 | 2.1.2 | FALSE | FALSE | 2018-03-15 | CRAN (R 3.6.1) |
| xfun | 0.12 | 0.12 | FALSE | FALSE | 2020-01-13 | CRAN (R 3.6.1) |
| xml2 | 1.2.2 | 1.2.2 | FALSE | FALSE | 2019-08-09 | CRAN (R 3.6.1) |
| xtable | 1.8.4 | 1.8-4 | FALSE | FALSE | 2019-04-21 | CRAN (R 3.6.1) |
| yaml | 2.2.1 | 2.2.1 | FALSE | FALSE | 2020-02-01 | CRAN (R 3.6.2) |
---
title: "Cognitive Longitudinal Outcomes by Program --PDSA Cycle 3"
output:
flexdashboard::flex_dashboard:
social: [ "menu" ]
# orientation: rows
vertical_layout: fill
source_code: embed
# css: ../common/style-cqi-cycle-4.css
# theme: cosmo
theme: journal
---
```{r, echo=F, message=F}
# cat("Working directory: ", getwd())
library(knitr)
library(flexdashboard)
opts_knit$set(root.dir = '../../') #Don't combine this call with any other chunk -especially one that uses file paths.
```
```{r set-options, echo=F}
# cat("Working directory: ", getwd())
report_render_start_time <- Sys.time()
opts_chunk$set(
results = 'show',
comment = NA,
tidy = FALSE,
# dpi = 400,
# out.width = "650px", #This affects only the markdown, not the underlying png file. The height will be scaled appropriately.
fig.width = 6,
fig.height = 6,
fig.path = 'figure-dashboard-png/'
)
echo_chunks <- FALSE #Toggle for debugging.
message_chunks <- FALSE #Toggle for debugging.
options(width = 100) #So the output is 25% wider than the default.
read_chunk("./analysis/dashboard-1/dashboard-1.R") #This allows knitr to call chunks tagged in the underlying *.R file.
```
```{r load-sources, echo=echo_chunks, message=message_chunks}
```
```{r load-packages, echo=echo_chunks, message=message_chunks}
```
```{r declare-globals, echo=echo_chunks, results='show', message=message_chunks}
```
```{r rmd-specific, echo=echo_chunks, message=message_chunks}
# Put presentation-specific code in here. It doesn't call a chunk in the codebehind file.
# It should be rare (and used cautiously), but sometimes it makes sense to include code in Rmd
# that doesn't live in the codebehind R file.
```
```{r load-data, echo=echo_chunks, results='show', message=message_chunks}
```
```{r tweak-data, echo=echo_chunks, results='show', message=message_chunks}
```
Headline
=============================================
This dashboard helps facilitate the CQI analyses VIHA E.C.R. (early cognitive recline) project.
Overall {.tabset data-width=300}
---------------------------------------------
### Notes
1. The current report covers `r scales::comma(nrow(ds))` total subject-event records for `r dplyr::n_distinct(ds$county)` unique counties (`r paste(sort(unique(ds$county)), collapse=", ")`).
1. The year of collection ranges from `r min(ds$year, na.rm=T)` to `r max(ds$year, na.rm=T)`.
1. The selected county is `r county_name_focus` (id value `r county_id_focus`).
{.tabset}
---------------------------------------------
```{r headline-graph, echo=echo_chunks, results='asis', message=message_chunks}
```
Tables
=============================================
{.tabset}
---------------------------------------------
### Tables - County-Year
```{r tables-county-year, echo=echo_chunks, message=message_chunks}
```
### Tables - County
```{r tables-county, echo=echo_chunks, message=message_chunks}
```
### Tables - Annotation
```{r tables-annotation, echo=echo_chunks, message=message_chunks}
```
Spaghetti
=============================================
{.tabset}
---------------------------------------------
```{r spaghetti, echo=echo_chunks, message=message_chunks, results='asis', fig.height=10, fig.width=20}
```
Marginals
=============================================
{.tabset}
---------------------------------------------
```{r marginals, echo=echo_chunks, message=message_chunks, results='asis'}
```
Documentation
=============================================
{.tabset}
---------------------------------------------
### Explanation -Current PDSA
#### SMART Aim
By implementing plans for self-care activities with established clients, primary caregivers will see a mean score reduction of at least 4 points on the ECR after 4 months of self-care activities by Dec 1, 2018.
#### Measures
* **Outcome**: Parent Stress
* Pre- and Post- Parent Stress Scale score change
* **Process**: Completed Resiliency Plans
* *Numerator*: Count of clients who completed their designated self-care activity
* *Denominator*: Count of clients with a visist in a given week
* **Disruptor**: Cultural issues preventing participation, toxic stress, family catastrophe
#### Spaghetti Notes
* **To be added**:
* Post score plots
* Pre-post comparisons
* Splitting out new clients from old clients to see if differences are more or less prominent
* **Mean PSS Scores - Pre**:
* Each blue dot represents a single client's PSS score on the pre measure
* The orange dots (connected by the red line) represent the mean PSS score for all clients on a given week.
* Dot size is proportional to the number of clients who had a pre-PSS score.
* **Stress Activity - Success**:
* *Numerator*: Number of clients who indicated having completed their self-care activity
* *Denominator*: All clients who responded to the self-care question (Yes/No to self-care)
* *Dot size*: The dot size is proportional to the number of clients who responded to that question on a given week.
#### Resources
* [Current PDSA](https://docs.google.com/document/d/1IcwCCkr1EkoeBJpEKdF2v-E0gKI6wGacCv9oZU1CE7I/edit#) (This is accessible only to CQI participants.)
### Explanation -All CQI Dashboards
```{r, child = "../common/dashboard/documentation-all-dashboards-1.Rmd"}
```
### Glossary
```{r, child = "../common/dashboard/documentation-glossary-1.Rmd"}
```
### Tips
```{r, child = "../common/dashboard/documentation-tips-1.Rmd"}
```
### Config
```{r, child = "../common/dashboard/documentation-config-1.Rmd"}
```